Bonnie Lysyk says in her annual report that could hurt the university's core function and reputation.
She makes 26 recommendations to improve oversight and policies for research projects.
One suggestion is that the university make expectations more clear with more detailed performance measures and targets.
Lysyk also says the university should regularly review research policies, many of which she notes have not been updated in several years.
The audit did not look at how research money was administered — the university had nearly $23 million of research revenue in 2011-2012.
The university asked for the auditor's review in large part because questions were raised about how more than $2 million was spent at the university-based International Performance Assessment Centre for the Geologic Storage of Carbon Dioxide, commonly known as IPAC-CO2.
When it was starting up in 2008, the IPAC centre got into a sole-sourced IT deal with Climate Ventures Inc.
A forensic investigation by Myers Norris Penny found there was a conflict of interest because two people, including acting managing director Malcolm Wilson, held seats on both the IPAC and Climate Ventures boards.
An internal memo said the greatest part of the money billed for IT services was "spent for no acceptable business reason."
The province cut funding to the centre earlier this year and it wound up operations.
University of Regina president Vianne Timmons said on May 30 that she had already seen the auditor's recommendations and that the school "absolutely" accepts them. Timmons says the university has a lot of work to do and hopes to implement the changes within 18 months.